changeset 0:93a6f5eb2f9a draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/intarna.xml	Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,40 @@
+<tool id="exparna" name="ExpaRNA" version="0.1.0">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="1.2.5">intarna</requirement>
+        <requirement type="package" version="1.8.5">vienna_rna</requirement>
+    </requirements>
+    <command>
+IntaRNA
+-m $query_file
+-t target_file
+    </command>
+    <stdio>
+        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
+    </stdio>
+    <inputs>
+        <param format="fasta" name="query_file" type="data" label="Query ncRNA Fasta File" />
+        <param format="fasta" name="target_file" type="data" label="Target RNA Fasta File" />
+        
+    </inputs>
+    <outputs>
+        <data format="txt" name="output" label="" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>**What it does**
+IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions.
+
+Anke Busch, Andreas S. Richter, and Rolf Backofen
+IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions
+Bioinformatics, 24 no. 24 pp. 2849-56, 2008
+Andreas S. Richter, Christian Schleberger, Rolf Backofen, and Claudia Steglich
+Seed-based IntaRNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1
+Bioinformatics, 26 no. 1 pp. 1-5, 2010
+
+**Output**
+    </help>
+</tool>

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fasta	Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,4 @@
+>ncRNA1
+AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU
+>ncRNA2
+ACUGAGGUACGAUCGUGGCAGGGCCUUUGACUGACUUUCGUACUUU

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example.fasta~	Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,4 @@
+>ncRNA1
+AGGAUGGGGGAAACCCCAUACUCCUCACACACCAAAUCGCCCGAUUUAUCGGGCUUUUUU
+>ncRNA2
+ACUGAGGUACGAUCGUGGCAGGGCCUUUGACUGACUUUCGUACUUU

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/example2.fasta	Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,8 @@
+>mRNA1
+UUUAAAUUAAAAAAUCAUAGAAAAAGUAUCGUUUGAUACUUGUGAUUAUACUCAGUUAUA
+CAGUAUCUUAAGGUGUUAUUAAUAGUGGUGAGGAGAAUUUAUGAAGCUUUUCAAAAGCUU
+GCUUGUGGCACCUGCAACUCUUGGUCUUUUAGCACCAAUGACCGCUACUGCUAAU
+>mRNA2
+UGCUUCUUAGUAAUGGCCAGCUCGGGGAUUUGGAACUGGUGGUUGUUAAUUCUAGGCAAA
+UAGAUUAAAAUUAAAUUACUCAAAUUGUGUGACGAGUUUUAUGAAGCUUUUUAAAAGCUU
+GUUGGUAGCUCCAGCAACGAUUGGGCUACUAGCUCCAUUUUCAACGUUUGCUGGC

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fasta~	Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,4 @@
+>AF165050.379
+UUGGGGGCGACAUUCCACCAUAGAUAAUUCCCCUGUGAGGAAUUACUGUUUUAACGCAGAAAGCGUUUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCUUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGAUGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCUAAACCCCAAAGAAAAACCAAACGUAACACCAACCG
+>D45172.391
+GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUAGAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUCAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCGAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCAUCAUGAGCACAAAUCCAAAACCCCAAAGAAAAAUCAAACGUAACACCAACCG

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Tue Jan 14 15:48:33 2014 -0500
@@ -0,0 +1,9 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="vienna_rna" version="1.8.5">
+        <repository changeset_revision="18c7086dbb43" name="package_vienna_rna_1_8" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="intarna" version="1.2.5">
+        <repository changeset_revision="6d5160860a70" name="package_intarna_1_2" owner="bgruening" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>